Plot simulation result

# S3 method for seiqhrf
plot(
  x,
  method = NULL,
  comp_remove = "none",
  time_limit = 90,
  ci = TRUE,
  sep_compartments = FALSE,
  trans = FALSE,
  known = NULL,
  start_date = ymd("2020-03-21"),
  show_start_date = FALSE,
  x_axis = "Days since beginning of epidemic",
  plot_title = "SEIQHRF",
  return_df = TRUE,
  market.share = 0.04,
  icu_percent = 0.1,
  total_population = NULL,
  ...
)

Arguments

x

An seiqhrf object returned from function seiqhrf.

method

If "times", plot Duration frequency distributions. If "weekly_local", plot local weekly estimates from simulation. If NULL, plot sirplus plots.

comp_remove

Compartments to remove. Suggest c(s.num, r.num)

time_limit

Number of steps (days) to plot.

ci

T/F to include 95% confidence intervals in sirplus plot.

sep_compartments

T/F use faceting to show each compartment in a separate plot, only works if plotting a single simulation.

trans

Y-axis transformation (e.g. log2, log10). Default = none.

known

Dataframe with known compartment numbers to plot alongside projections

start_date

Date for day 0. Default: ymd("2020-03-21"),

show_start_date

First date to show in plots. Use ymd format. If FALSE, shows from step 1. Default: FALSE

x_axis

Title for x-axis. Default: 'Days since beginning of epidemic'

plot_title

Title for whole plot. Default: 'SEIQHRF plot'

return_df

In effect only when method == "weekly", if TRUE returns also the dataframe used for plotting as well as the ggplot object.

market.share

between 0 and 1, percentage of local hospital beds in the simulated unit (e.g. state)

icu_percent

between 0 and 1, percentage of patients that should go to ICU among the ones that need hospitalization

total_population

True population size, needed only if simulation size is smaller than the true population size due to computational cost etc.

...

Additional parameters